--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/JunctionDiff-vs-background.xml	Mon Aug 03 05:01:15 2015 -0400
@@ -0,0 +1,72 @@
+<tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.6">
+	<description> Filter SVs based on presence in VN set </description>
+	
+	<requirements>		
+		<requirement type="package" version="1.7">cgatools</requirement>
+	</requirements>
+	
+	<command interpreter="bash">
+	JunctionDiff-vs-background.sh 
+		--variants $variants 
+		--reference ${reference.fields.reference_crr_cgatools} 
+		#if $virtnorm.VNset == "diversity"
+			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list} 
+		#else
+			--VN_junctions ${reference.fields.VN_genomes_junctionfile_list_1000G} 
+		#end if
+		--cgatools_binary cgatools
+		--outputfile_filtered $output_filtered 
+		--scoreThresholdA $scoreThresholdA 
+		--scoreThresholdB $scoreThresholdB 
+		--distance $distance 
+		--minlength $minlength					
+	</command>
+	
+	<inputs>
+		<!--select build-->
+		<param name="reference" type="select" label="Select Build">
+			<options from_data_table="virtual_normal_correction" />
+			<filter type="data_meta" ref="variants" key="dbkey" column="0" />
+		</param>
+		<conditional name="virtnorm" >
+		<param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples">
+			<option value="diversity" selected="true"> CG Diversity Panel and trios (54 Genomes) (hg18/hg19) </option>
+			<option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
+		</param>
+		</conditional>
+		<param name="variants" type="data" format="tabular" label="CG Junctions file"/>
+		<param name="scoreThresholdA" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from input genome"/>
+		<param name="scoreThresholdB" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from background genomes"/>
+		<param name="distance" type="text" value="200" label="Maximum distance between coordinates of potentially compatible junctions."/>		
+		<param name="minlength" type="text" value="500" label="Minimum deletion junctions length to be included into the difference file."/>
+		<param name="report" type="select"  label="Generate report file?">
+			<option value="N" selected="true"> No </option>
+			<option value="Y"> Yes </option>
+		</param>
+		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>		
+	</inputs>
+
+  <outputs>
+       <data format="tabular" name="output_filtered" label="${fname} Filtered junctions for ${tool.name} on  ${on_string}"/>		
+       <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on  ${on_string}">
+       	<filter> report == "Y" </filter>
+       </data>			  
+  </outputs>
+
+	<help> 
+**What it does**
+
+
+
+**Input Files**
+Complete Genomics Junctions file
+
+**Output Files**
+Junctions remaining after filtering
+
+
+	</help>
+
+</tool>
+
+